Data Description & Quality Assessment

*GC content of each library showing uneven and 'spikey' patterns. Peaks on the RHS indicate potential incomplete rRNA removal, whilst the other peaks indicate possible excessive PCR cycles and high levels of duplicated sequences.*

GC content of each library showing uneven and ‘spikey’ patterns. Peaks on the RHS indicate potential incomplete rRNA removal, whilst the other peaks indicate possible excessive PCR cycles and high levels of duplicated sequences.

*Estimated duplication levels within each sample. Higher than expected sequence duplication rates were observed, particularly for sequences present greater than 10,000 times. Sample 179_F and 187_F were of particular concern, however this is also suggestive of incomplete rRNA removal*

Estimated duplication levels within each sample. Higher than expected sequence duplication rates were observed, particularly for sequences present greater than 10,000 times. Sample 179_F and 187_F were of particular concern, however this is also suggestive of incomplete rRNA removal

*STAR Alignment summary showing very low levels of unique alignments, which is again suggestive of incomplete rRNA removal. Uniquely mapping reads are within the range usually seen after summarising to genes, indicating that final gene-level counts may be a little lower than is optimal.*

STAR Alignment summary showing very low levels of unique alignments, which is again suggestive of incomplete rRNA removal. Uniquely mapping reads are within the range usually seen after summarising to genes, indicating that final gene-level counts may be a little lower than is optimal.

After assignment to transcripts, the library sizes ranged between 6,954,273 and 14,565,667 reads

Gene Expression Analysis

PCA with colours indicating treatment group and point sizes indicating sample weights. A trend from left to right along PC1 tracked somewhat with library size, with all points along PC1 appearing in order of library size for each respective treatment group. Point sizes are proportional to sample weights.

*Correlation between library size and PC1. A simple regression line is also shown for illustrative purposes*

Correlation between library size and PC1. A simple regression line is also shown for illustrative purposes

Differentially Expressed Genes

Differentially expressed (DE) genes were detected using a slight variation from the common null hypothesis. Instead of testing \(H_0: \log FC = 0\) which tests for the point value zero, the null hypothesis was defined as being within the range [\(-\tau, \tau\)], with \(\tau\) set at the default value of \(\log_2 1.2\). This additionally saves filtering any detected DE genes based on fold-change, as is common practice in many workflows.

\[ H_0: |\log FC| \leq \tau \\ vs \\ H_A: |\log FC| > \tau \]

  • After analysis, 2 genes were found to be differentially expressed using an FDR of 0.05.
  • Using a less stringent FDR threshold of 20.0% gave weak-to-moderate support for 18 genes as potentially DE.
Top 18 most highly-ranked genes when sorting by p-value. This represents an FDR of up to 20.0%.logFC > 0 indicates up regulation in diabetic samples relative to control
ID Name logFC AveExpr t P.Value FDR Location
ENSRNOG00000047551 Pnpla2 -7.192 0.1297 -13.03 3.366e-06 0.02817 1:213997709-214002815:(+)
ENSRNOG00000050004 LOC100909761 6.553 -1.417 12.54 4.281e-06 0.02817 9:37727942-37747514:(+)
ENSRNOG00000032832 Mmp10 3.502 2.164 8.801 3.739e-05 0.164 8:5734348-5742243:(+)
ENSRNOG00000032626 Mmp3 3.612 4.589 8.212 5.869e-05 0.1722 8:5676665-5698579:(+)
ENSRNOG00000002802 Cxcl1 4.895 1.902 7.867 8.313e-05 0.1722 14:18743685-18745457:(-)
ENSRNOG00000010278 Il6 4.79 0.1518 7.816 8.615e-05 0.1722 4:3043231-3047807:(+)
ENSRNOG00000060849 Rcor2 -5.115 -1.303 -7.702 9.595e-05 0.1722 1:222519615-222524779:(+)
ENSRNOG00000000239 Ccl7 2.751 2.899 7.271 0.0001171 0.1722 10:69423086-69424979:(+)
ENSRNOG00000007545 Angptl4 1.854 3.859 7.069 0.0001249 0.1722 7:18627808-18634079:(-)
ENSRNOG00000024705 Rarres2 2.479 4.591 6.783 0.0001748 0.1722 4:78205812-78208767:(-)
ENSRNOG00000015992 Ccl20 4.455 0.1233 6.931 0.0001792 0.1722 9:88918433-88921001:(+)
ENSRNOG00000048321 Tnfsf8 2.079 2.527 6.607 0.0001954 0.1722 5:79664765-79691258:(-)
ENSRNOG00000020953 Ms4a7 1.993 2.448 6.576 0.0001987 0.1722 1:227490777-227506822:(-)
ENSRNOG00000062228 LOC100359515 4.669 0.8863 6.785 0.0002066 0.1722 10:64762907-64790306:(-)
ENSRNOG00000002792 Cxcl2 7.725 2.716 6.866 0.0002126 0.1722 14:18731378-18733391:(-)
ENSRNOG00000022839 Ifit3 3.289 6.303 6.634 0.000217 0.1722 1:252906234-252911382:(+)
ENSRNOG00000028043 Cxcl3 6.554 2.794 6.725 0.0002345 0.1722 14:18820168-18839595:(-)
ENSRNOG00000016812 Adamts16 3.102 0.7835 6.528 0.0002355 0.1722 1:35067490-35198939:(+)
*Average expression against logFC. Confidently significant genes (FDR < 0.05) are indicated in red, whilst others are labelled to an FDR of 20.0%*

Average expression against logFC. Confidently significant genes (FDR < 0.05) are indicated in red, whilst others are labelled to an FDR of 20.0%

*Volcano plot with confidently significant genes shown in red. Genes to an FDR of20.0%are labelled.*

Volcano plot with confidently significant genes shown in red. Genes to an FDR of20.0%are labelled.

*Expression values for genes to an FDR of 20.0%. Genes are shown in order of significance. Jitter has been added to the x-axis*

Expression values for genes to an FDR of 20.0%. Genes are shown in order of significance. Jitter has been added to the x-axis

Gene Set Enrichment

Given the relatively small number of DE genes, the most suitable enrichment analysis was chosen to be GSEA as this works on a ranked list with no requirement for formal consideration of genes as differentially expressed. This approach walks through a ranked list and checks to see if genes with a given gene-set are clustered at either end of the ranked list. If no correlation between the gene-set and the experiment is evident, they should be evenly spread throughout the list. Otherwise they could reasonably be expected to show directional bias. As this is a fairly broad view analysis, gene sets were chosen as defined for human EntrezGene identifiers, then these were mapped to Ensembl rat identifiers. All gene-sets are described at the Broad Institute

Four gene sets were chosen:

Genes were ranked by t-statistic, and all results were permuted 1,000,000 times for greater precision in results.

An additional 3 points of caution should be noted:

  1. This method will almost always return results and may contain false positives. As a result, very strict p-value adjustment strategies will be used.
  2. There is an inherent bias towards defined pathways. Unknown pathways are simply not tested
  3. Many gene-sets will overlap considerably and untangling which are key pathways can be challenging

Hallmark Gene Sets

Top 14 enriched Hallmark gene-sets using a Bonferroni-adjusted p-value < 0.01 for stringency. The normalised enrichment score indicates which end of the ranked list appeared to be enriched, with negative values indicating the down regulated genes. The number of genes in the gene-set are also indicated, as are the number of genes at the point of maximum enrichment. The most highly ranked genes before the point of the maximal enrichment are given in the final column.
Pathway NES \(p\) \(p_{adj}\) size sizeAtMax Genes
HALLMARK_INTERFERON_GAMMA_RESPONSE 1.673 1.151e-06 5.757e-05 181 37 Il6,Ccl7,Ifit3,Ptgs2,C1s,Isg15,Sod2,Tnfaip6,Socs3,Pde4b,Mx1,Cfb,Ifitm3,Upp1,Ccl2,Hif1a,Ifit2,Usp1…
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 1.83 1.154e-06 5.769e-05 178 84 Mmp3,Il6,Cxcl6,Tgfbi,Fbln2,Htra1,Acta2,Mgp,Ptx3,Itga5,Timp1,Mfap5,Col5a3,Fbn2,Col8a2,Col3a1,Tfpi2…
HALLMARK_TNFA_SIGNALING_VIA_NFKB 1.928 1.156e-06 5.782e-05 175 87 Il6,Tlr2,Cxcl6,Il1b,Ptgs2,Sod2,Junb,Tnfaip6,G0s2,F3,Socs3,Il1a,Pde4b,Olr1,Gfpt2,Ptx3,Ier3,Inhba,C…
HALLMARK_MYOGENESIS 1.78 1.163e-06 5.816e-05 168 72 LOC108348074,Mylpf,Myh8,Tnni2,Myoz1,Myl1,Myh1,Ckm,Myom2,Eno3,Tnnt3,Pgam2,Mb,Tnnc2,Cox6a2,Pvalb,Co…
HALLMARK_INFLAMMATORY_RESPONSE 1.936 1.169e-06 5.845e-05 162 59 Il6,Ccl7,Tlr2,Cxcl6,Il1b,Has2,Il1r1,Tnfaip6,F3,Il1a,Pde4b,Slc7a2,Olr1,Ifitm3,Mefv,Itga5,Timp1,Slc…
HALLMARK_COMPLEMENT 1.697 2.336e-06 0.0001168 163 36 Il6,Ctsl,C1s,Ctss,F3,Plat,Ctsc,Olr1,Cfb,Timp1,C1qa,Tfpi2,Col4a2,Maff,C2,Zfpm2,Pla2g7,Mmp14,Lgmn,P…
HALLMARK_COAGULATION 1.777 3.802e-06 0.0001901 92 29 Mmp3,Ctsl,Cfi,C1s,F3,Plat,Htra1,Olr1,Cfb,Timp1,C1qa,LOC100911545,Tfpi2,Maff,C2,Mmp2,Ctsk,Mmp14,Lg…
HALLMARK_HEME_METABOLISM -2.074 7.816e-06 0.0003908 187 80 Bpgm,Ctse,Mkrn1,Minpp1,Epb41,Fech,Foxo3,Klf1,Abcb6,LOC103689947,Ranbp10,Sptb,Alas2,Slc4a1,Tent5c,…
HALLMARK_MYC_TARGETS_V1 -1.8 8.052e-06 0.0004026 193 45 Pabpc4,Tufm,Pold2,Ccna2,Srsf2,Ran,Cdc20,Mcm5,Trim28,Impdh2,LOC100911372,Hnrnpd,Ncbp2,Lsm2,Mcm7,Cs…
HALLMARK_E2F_TARGETS -2.283 8.337e-06 0.0004169 200 94 Cdc25b,Birc5,Cdca3,E2f8,Ncapd2,H2afx,Kif18b,Stmn1,Rrm2,Pold2,Srsf2,Rad51ap1,Aurka,Ran,Dclre1b,Zw1…
HALLMARK_G2M_CHECKPOINT -2.004 8.382e-06 0.0004191 201 70 Hira,Cdc25b,Birc5,H2afx,Stmn1,Tent4a,Ccnf,Ccna2,Srsf2,Tgfb1,Aurka,Plk1,Cdc20,Mcm5,E2f4,Traip,Nek2…
HALLMARK_HYPOXIA 1.56 6.203e-05 0.003102 184 57 Il6,Angptl4,Errfi1,LOC100911515,Tgfbi,F3,Eno3,Pgam2,Ddit4,Slc2a1,Prdx5,Pygm,Tgm2,Ier3,Atf3,Plin2,…
HALLMARK_MITOTIC_SPINDLE -1.528 8.382e-05 0.004191 201 31 Epb41,Birc5,Sept9,Anln,Shroom2,Tubgcp2,Aurka,Plk1,Itsn1,Nek2,Racgap1,Arhgef12,Pcnt,Cep131,Tlk1,Mi…
HALLMARK_IL6_JAK_STAT3_SIGNALING 1.667 9.709e-05 0.004854 79 24 Il6,Ccl7,Tlr2,Il1b,Il1r2,Il1r1,Cxcl13,Socs3,LOC100911545,Cd14,Osmr,Il2ra,Tnfrsf12a,Il4r,LOC103694…
*Enrichment score for the most highly ranked hallmark geneset*

Enrichment score for the most highly ranked hallmark geneset

C2 Curated Gene Sets

As this was a larger database of gene-sets, only those with between 15 & 500 genes were tested.

Top 20 enriched C2 gene-sets using a Bonferroni-adjusted p-value < 0.01 for stringency. The normalised enrichment score indicates which end of the ranked list appeared to be enriched, with negative values indicating the down regulated genes. The number of genes in the gene-set are also indicated, as are the number of genes at the point of maximum enrichment. The most highly ranked genes before the point of the maximal enrichment are given in the final column.
Pathway NES \(p\) \(p_{adj}\) size sizeAtMax Genes
REN_ALVEOLAR_RHABDOMYOSARCOMA_DN 1.769 1.051e-06 0.003658 400 116 S100a6,Cttn,Ptges,C1s,Tspo,Tgfbi,Rhoc,Plat,Htra1,Ptx3,Itga5,Timp1,Col8a2,Tfpi2,Gpr176,Inhba,Osmr,…
NABA_MATRISOME_ASSOCIATED 1.756 1.056e-06 0.003675 380 156 Mmp3,Il6,Ccl7,Angptl4,Tnfsf8,Adamts16,Cxcl6,S100a6,Ctsl,C1qtnf7,Il1b,Slpi,Adamts15,Masp1,Adamts1,…
CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN 1.621 1.057e-06 0.003679 375 116 Ifit3,Tlr2,Cfi,Ptgs2,Slpi,C1s,Tgfbi,F3,Gpm6b,Plat,Ctsc,Il1a,Htra1,Il1rap,Cfb,Nxn,Upp1,Col4a1,Inhb…
BOQUEST_STEM_CELL_CULTURED_VS_FRESH_UP 1.679 1.058e-06 0.003683 371 120 Angptl4,Cfi,LOC108348074,Prg4,Sod2,Junb,Tnfaip6,Ctss,Flnc,Mx1,Rrad,Agtr1a,Ifitm3,LOC102553715,Mgp…
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP 1.736 1.075e-06 0.003741 318 117 Mmp3,Rarres2,LOC108348074,C1s,Il1r1,Tnfaip6,Ctss,Tgfbi,Fbln2,Htra1,Olr1,Gfpt2,Mfap5,C1qa,LOC49827…
RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN 1.633 1.082e-06 0.003764 300 97 S100a6,Adamts15,Gpm6b,Il1a,Htra1,Slc2a1,Col5a3,Upp1,Inhba,Hif1a,Rcan1,Tes,Cdkn1a,Trem1,Sdc1,Il20r…
WANG_SMARCE1_TARGETS_UP 1.794 1.116e-06 0.003884 229 91 Ifit3,Cfi,LOC108348074,Car4,C1s,Prg4,Il1r1,Tgfbi,Socs3,Plat,Acta2,Glipr2,Mgp,Ptx3,Mfap5,Col3a1,Ta…
HOSHIDA_LIVER_CANCER_SUBCLASS_S1 1.662 1.12e-06 0.003898 223 61 LOC108348074,Ctss,Ccl3,AABR07034739.1,Ctsc,Acta2,Mgp,Slc2a1,Crabp2,LOC498276,Col3a1,Col4a1,Rin2,T…
BOQUEST_STEM_CELL_UP 1.676 1.124e-06 0.00391 217 85 C1s,Tnfaip6,F3,Htra1,Cfb,LOC102553715,Gfpt2,Mgp,Ptx3,Crabp2,Timp1,Mfap5,Col3a1,Col14a1,Inhba,Col1…
VERHAAK_GLIOBLASTOMA_MESENCHYMAL 1.706 1.125e-06 0.003915 215 90 Tlr2,Il1r1,Tgfbi,Ctsc,Itga5,Timp1,LOC498276,Col8a2,Dsc2,Sypl1,Cd14,Lamb1,Msr1,Folr2,Tes,Il4r,Bnc2…
MCLACHLAN_DENTAL_CARIES_UP 1.673 1.128e-06 0.003926 210 73 Il6,Cfi,Il1b,LOC108348074,Ptgs2,Slpi,Sod2,Cxcl13,Tnfaip6,Ctss,G0s2,Ccl3,Socs3,Ctsc,Cfb,Mgp,Timp1,…
MARKEY_RB1_ACUTE_LOF_DN 1.67 1.133e-06 0.003944 203 55 Mmp3,Ccl7,Ifit3,Isg15,Sod2,Tgfbi,Pcsk5,Ccl3,Socs3,RGD1559482,AABR07030793.1,Crabp2,Prdx5,LOC49827…
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP 1.725 1.147e-06 0.003992 186 67 Rarres2,LOC108348074,C1s,Adamts1,Ccl21,Ctsc,Acta2,Cfb,LOC102553715,C1qa,Col8a2,LOC100911545,Col3a…
ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF 1.686 1.15e-06 0.004001 183 68 Il6,Il1b,Ptgs2,Junb,Nfkbiz,Socs3,Il1a,Olr1,Il1rap,Slc2a1,Pygm,Mmp19,Ier3,Atf3,Phlda1,Cebpd,Fos,Ma…
ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_UP 1.746 1.154e-06 0.004016 178 54 Ifit3,Tlr2,Il1b,Il1r2,Sod2,Tnfaip6,G0s2,Nfkbiz,Socs3,Il1a,Slc7a2,Olr1,Ptx3,Ddit4,Inhba,Atf3,Maff,…
BROWN_MYELOID_CELL_DEVELOPMENT_UP 1.864 1.18e-06 0.004105 152 48 Tlr2,S100a6,Il1b,Il1r2,Junb,Ctss,Tgfbi,Tnnt3,Olr1,Glipr2,LOC498276,Upp1,Cebpd,C2,Il1rn,Dgat2,Trem…
GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_UP 1.733 1.199e-06 0.004172 135 50 Angptl4,Errfi1,Vwa1,LOC100911515,Nfkbiz,Slc2a1,Prdx5,Atf3,Phlda1,Ankrd1,Fos,Rcan1,AC094212.1,Dusp…
NABA_ECM_REGULATORS 1.771 1.2e-06 0.004176 134 61 Mmp3,Adamts16,Ctsl,Slpi,Adamts15,Masp1,Adamts1,Ctss,Pcsk5,AABR07049085.1,Plat,Ctsc,Htra1,Tll1,Tgm…
MIKKELSEN_MEF_LCP_WITH_H3K4ME3 1.83 1.231e-06 0.004285 112 51 Ccl7,Masp1,Col3a1,Mmp19,Inhba,Ccl2,Rufy4,LOC108348048,Nnmt,Ccn5,Mab21l3,Il1rn,Lum,Il18rap,Gal3st4…
ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION 1.986 1.234e-06 0.004294 110 50 Il6,Tlr2,Cxcl6,Il1b,Il1r2,Isg15,Sod2,Junb,Nfkbiz,Ccl3,F3,Socs3,Il1a,Gk,Clec4e,Mefv,Tgm1,Timp1,LOC…
*Enrichment score for the most highly ranked C2 genesets*

Enrichment score for the most highly ranked C2 genesets

C5 GO Gene Sets

For analysis of GO-related gene-sets the maximal set size was reduced to 200 to ensure the more generic & high-level terms were excluded.

Top 15 enriched C5 gene-sets using a Bonferroni-adjusted p-value < 0.01 for stringency. The normalised enrichment score indicates which end of the ranked list appeared to be enriched, with negative values indicating the down regulated genes. The number of genes in the gene-set are also indicated, as are the number of genes at the point of maximum enrichment. The most highly ranked genes before the point of the maximal enrichment are given in the final column.
Pathway NES \(p\) \(p_{adj}\) size sizeAtMax Genes
GO_MUSCLE_SYSTEM_PROCESS 1.925 1.141e-06 0.004073 194 73 LOC100909761,Il1b,Agtr2,Mylpf,Myh8,LOC103692716,Mybpc2,Tnni2,Myl1,Myh1,Myom2,Tnnt3,Pgam2,Acta2,Ht…
GO_REGULATION_OF_ERK1_AND_ERK2_CASCADE 1.708 1.159e-06 0.004138 173 46 Il6,Ccl7,Il1b,Errfi1,Scimp,Ccl3,Ccl21,Havcr2,Glipr2,Ndrg4,Htr2b,Ccl2,Atf3,Bmper,LOC103689974,Tnfs…
GO_CONTRACTILE_FIBER 1.926 1.168e-06 0.00417 163 63 LOC100909761,Mylpf,Myh8,Abra,Tnni2,Myl1,Myh1,Myom2,Flnc,Tnnt3,Acta2,Pde4b,Tnnc2,Ankrd23,Cmya5,Tmo…
GO_MUSCLE_CONTRACTION 1.974 1.172e-06 0.004183 160 67 LOC100909761,Mylpf,Myh8,LOC103692716,Mybpc2,Tnni2,Myl1,Myh1,Myom2,Tnnt3,Pgam2,Acta2,Htr7,Mb,Tnnc2…
GO_CELLULAR_RESPONSE_TO_BIOTIC_STIMULUS 1.716 1.194e-06 0.004264 139 42 Il6,Tlr2,Il1b,Arg1,LOC497963,Tspo,Ccl3,Pde4b,Havcr2,Ccl2,Cd14,Hif1a,Ankrd1,Wnt5a,Irak2,Nlrp3,Lbp,…
GO_POSITIVE_REGULATION_OF_RESPONSE_TO_WOUNDING 1.829 1.235e-06 0.004408 110 41 Il6,Ccl7,Tlr2,Il1b,Ptgs2,Ccl3,F3,Agtr1a,Ccl2,Osmr,LOC103689974,Tnfsf11,Wnt5a,Lbp,Osm,Pla2g7,Ccl12…
GO_RESPONSE_TO_INTERFERON_GAMMA 1.898 1.243e-06 0.004437 105 38 Ccl7,LOC497963,Ccl3,Ccl21,Ifitm3,AC099450.1,Mefv,Ccl2,Oas1a,Wnt5a,Gbp2,Acod1,Icam1,Aqp4,Ccl12,Ccl…
GO_RESPONSE_TO_INTERLEUKIN_1 1.787 1.281e-06 0.004573 85 35 Il6,Ccl7,Has2,Il1r1,Ccl3,Ccl21,Il1rl2,Ccl2,Hif1a,Ankrd1,Irak2,Acod1,Icam1,Ccl12,Ccl9,Ccl11,Cebpb,…
GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA 1.927 1.283e-06 0.00458 84 33 Ccl7,LOC497963,Ccl3,Ccl21,AC099450.1,Ccl2,Oas1a,Wnt5a,Gbp2,Acod1,Icam1,Aqp4,Ccl12,Ccl9,Ccl11,Oas3…
GO_LEUKOCYTE_CHEMOTAXIS 1.814 1.299e-06 0.004639 77 33 Il6,Ccl7,Il1b,Cxcl13,Ccl3,Ccl21,Pde4b,Ccl2,LOC103689974,Tnfsf11,Folr2,Lbp,Trem1,Ccr5,Ccl12,Ccl9,C…
GO_POSITIVE_REGULATION_OF_INFLAMMATORY_RESPONSE 1.873 1.304e-06 0.004655 75 35 Il6,Ccl7,Tlr2,Il1b,Ptgs2,Ccl3,Agtr1a,Ccl2,Osmr,LOC103689974,Tnfsf11,Wnt5a,Lbp,Osm,Pla2g7,Ccl12,Cc…
GO_CELLULAR_RESPONSE_TO_INTERLEUKIN_1 1.888 1.332e-06 0.004757 64 31 Il6,Ccl7,Has2,Il1r1,Ccl3,Ccl21,Il1rl2,Ccl2,Hif1a,Ankrd1,Irak2,Acod1,Icam1,Ccl12,Ccl9,Ccl11,Cebpb,…
GO_CYTOKINE_RECEPTOR_BINDING 1.67 2.349e-06 0.008386 157 50 Il6,Ccl7,Tnfsf8,Cxcl6,Il1b,Cxcl13,Ccl3,Ccl21,Il1a,Il1rap,Itga5,Nol3,Inhba,Ccl2,Rasl11b,LOC1036899…
GO_DEFENSE_RESPONSE_TO_VIRUS 1.734 2.426e-06 0.00866 125 26 Il6,Ifit3,Isg15,Ifit1bl,Mx1,Ifitm3,Ddit4,Oas1a,Pmaip1,Ifit2,Nlrp3,Dhx58,Cd8a,Mx2,Oas3,Oasl,Plscr1…
GO_REGULATION_OF_CYTOKINE_SECRETION 1.736 2.502e-06 0.008933 100 38 Il6,Tlr2,Il1b,Agtr2,Ccl3,Il1a,Ssc5d,Havcr2,Clec4e,Htr2b,Cd14,Wnt5a,Nlrp3,Il4r,Tlr1,Cd274,Postn,Cd…
*Enrichment score for the most highly ranked C5 genesets*

Enrichment score for the most highly ranked C5 genesets

C7 Immunologic Signatures

Top 20 enriched C7 gene-sets using a Bonferroni-adjusted p-value < 0.01 for stringency. The normalised enrichment score indicates which end of the ranked list appeared to be enriched, with negative values indicating the down regulated genes. The number of genes in the gene-set are also indicated, as are the number of genes at the point of maximum enrichment. The most highly ranked genes before the point of the maximal enrichment are given in the final column.
Pathway NES \(p\) \(p_{adj}\) size sizeAtMax Genes
GSE42021_TCONV_PLN_VS_TREG_PRECURSORS_THYMUS_DN 1.785 1.143e-06 0.00557 192 49 Ccl7,Angptl4,Il1b,Errfi1,Ptgs2,Ptges,LOC103692716,Junb,Nfkbiz,Socs3,Il1a,Glipr2,Clec4e,LOC498276,…
GSE22935_WT_VS_MYD88_KO_MACROPHAGE_UP 1.733 1.144e-06 0.005574 191 58 Ptgs2,Icos,Tnn,Htra1,Mefv,Itga5,C1qa,Col16a1,Hif1a,LOC108348048,Tes,Ptgr1,Mmp2,M6pr,Emilin2,Vwa5a…
GSE22935_WT_VS_MYD88_KO_MACROPHAGE_48H_MBOVIS_BCG_STIM_DN 1.658 1.145e-06 0.005577 190 57 Aldh18a1,Il1r1,Rhoc,Socs3,Plat,C1qa,Col3a1,Brk1,Il1rl2,Crip1,Plin2,LOC108348048,Dpt,Tes,Vwa5a,Wls…
GSE42021_TREG_PLN_VS_CD24INT_TREG_THYMUS_UP 1.838 1.145e-06 0.005577 190 59 Il1b,Errfi1,Ptgs2,Ptges,LOC103692716,Junb,Nfkbiz,Socs3,Plat,Il1a,Glipr2,AABR07044940.1,Upp1,Cd14,…
GSE18281_SUBCAPSULAR_VS_CENTRAL_CORTICAL_REGION_OF_THYMUS_DN 1.688 1.146e-06 0.005584 188 52 Ifit3,Cxcl6,Ifit1bl,Nfkbiz,Socs3,Ctsc,Gk,Mefv,Itga5,Timp1,Upp1,Oas1a,Fos,Ifit2,Usp18,Samsn1,Cdkn1…
GSE22140_GERMFREE_VS_SPF_MOUSE_CD4_TCELL_DN 1.668 1.148e-06 0.005592 186 45 Ccl7,Tnfsf8,Ifit3,Il1b,Tgfbi,Ccl3,Htra1,Mx1,RGD1559482,AABR07030793.1,Ifitm3,AABR07044940.1,Ptx3,…
GSE27434_WT_VS_DNMT1_KO_TREG_DN 1.809 1.148e-06 0.005592 186 44 Ccl7,Il1b,Errfi1,Ptgs2,LOC103692716,Junb,Nfkbiz,Socs3,Il1a,Fbln2,Clec4e,Crabp2,Inhba,Cd14,Phlda1,…
GSE14769_UNSTIM_VS_60MIN_LPS_BMDM_DN 1.705 1.149e-06 0.005597 185 53 Ccl7,Tlr2,Il1b,Errfi1,Ptgs2,Sod2,F3,Clec4e,Ier3,Atf3,Cd14,Hif1a,Phlda1,Fos,Dusp16,Acod1,Icam1,Osm…
GSE3039_ALPHAALPHA_VS_ALPHABETA_CD8_TCELL_UP 1.725 1.149e-06 0.0056 184 52 Il6,Tlr2,Ctsl,Ptges,LOC100911515,Socs3,Htr7,Nxn,Slc2a1,LOC498276,Upp1,Ier3,Cd14,Phlda1,Maff,Uqcr1…
GSE22140_HEALTHY_VS_ARTHRITIC_GERMFREE_MOUSE_CD4_TCELL_DN 1.678 1.15e-06 0.005604 183 57 Ccl7,Tnfsf8,Ifit3,Tlr2,Il1b,Tgfbi,Ccl3,Mx1,AABR07044940.1,Ptx3,Timp1,LOC498276,Upp1,Ier3,Crip1,Pm…
GSE14769_UNSTIM_VS_40MIN_LPS_BMDM_DN 1.757 1.152e-06 0.005612 181 53 Ccl7,Tlr2,Errfi1,Ptgs2,Junb,Nfkbiz,Socs3,Pde4b,Clec4e,Ier3,Ccl2,Atf3,Cd14,Phlda1,Fos,Maff,Usp18,R…
GSE45365_NK_CELL_VS_CD11B_DC_DN 1.786 1.154e-06 0.005621 179 54 Il6,Il1b,Ptges,Junb,Nfkbiz,Pde4b,Olr1,Clec4e,Mefv,Ptx3,Timp1,Tgm2,Ier3,Cd14,Phlda1,Osmr,Fos,Maff,…
GSE14769_UNSTIM_VS_80MIN_LPS_BMDM_DN 1.766 1.155e-06 0.005625 178 59 Tlr2,Il1b,Isg15,Sod2,Adamts1,Clec4e,Tgm2,Atf3,Phlda1,Fos,Maff,Gbp2,Usp18,Arl5b,Il1rn,Acod1,Flrt3,…
GSE19198_CTRL_VS_IL21_TREATED_TCELL_24H_UP 1.764 1.155e-06 0.005625 178 54 Mmp3,Il6,Ccl7,Errfi1,Sod2,Il1a,Pde4b,Slc7a2,Ifitm3,Itga5,Timp1,Upp1,Tfpi2,Tgm2,Atf3,Hif1a,Plin2,M…
GSE46606_UNSTIM_VS_CD40L_IL2_IL5_1DAY_STIMULATED_IRF4HIGH_SORTED_BCELL_DN 1.723 1.155e-06 0.005625 178 42 Il6,Il1b,Errfi1,Ptgs2,Nfkbiz,Socs3,Pde4b,Rrad,Mefv,Ier3,Phlda1,Maff,Cdkn1a,Acod1,Icam1,Rgs1,Itpkc…
GSE34392_ST2_KO_VS_WT_DAY8_LCMV_EFFECTOR_CD8_TCELL_DN 1.696 1.156e-06 0.00563 177 68 Il6,Tlr2,Il1b,Isg15,Ifit1bl,Junb,Nfkbiz,F3,Slc7a2,Tll1,Slc2a1,Tgm2,Atf3,Phlda1,Ifit2,Usp18,Rcan1,…
GSE18281_CORTICAL_VS_MEDULLARY_THYMOCYTE_UP 1.731 1.156e-06 0.005634 176 58 Ifit3,Cxcl6,Arg1,Ptgs2,Slpi,Isg15,Ifit1bl,Ctss,Plat,Ctsc,Gk,Mx1,Ifitm3,Tgm2,Atf3,Cd14,Phlda1,Osmr…
GSE42021_TREG_PLN_VS_CD24HI_TREG_THYMUS_UP 1.829 1.158e-06 0.005642 174 55 Ccl7,Il1b,Errfi1,Ptgs2,LOC103692716,Junb,Nfkbiz,Socs3,Il1a,Fbln2,Clec4e,Crabp2,Upp1,Ier3,Cd14,Phl…
GSE7509_DC_VS_MONOCYTE_DN 1.667 1.159e-06 0.005646 173 36 Ifit3,Slpi,Ptges,Sod2,Tspo,Olr1,Clec4e,Inhba,Cd14,Gbp2,Usp18,Ccn5,Acod1,RGD1564937,Slfn4,Ets2,Anx…
GSE32986_CURDLAN_HIGHDOSE_VS_GMCSF_AND_CURDLAN_HIGHDOSE_STIM_DC_DN 1.72 1.159e-06 0.005646 173 58 Rarres2,Tlr2,Il1b,Ptgs2,Isg15,Sod2,Junb,Nfkbiz,Socs3,Il1a,Pde4b,Olr1,Rrad,Clec4e,Mefv,Itga5,Maff,…
*Enrichment score for the most highly ranked C7 genesets*

Enrichment score for the most highly ranked C7 genesets

Session Info

R version 3.6.1 (2019-07-05)

Platform: x86_64-pc-linux-gnu (64-bit)

locale: LC_CTYPE=en_AU.UTF-8, LC_NUMERIC=C, LC_TIME=en_AU.UTF-8, LC_COLLATE=en_AU.UTF-8, LC_MONETARY=en_AU.UTF-8, LC_MESSAGES=en_AU.UTF-8, LC_PAPER=en_AU.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_AU.UTF-8 and LC_IDENTIFICATION=C

attached base packages: grid, stats4, parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: fgsea(v.1.10.1), Rcpp(v.1.0.2), ggrepel(v.0.8.1), plyranges(v.1.4.3), rtracklayer(v.1.44.4), GenomicRanges(v.1.36.1), GenomeInfoDb(v.1.20.0), IRanges(v.2.18.2), S4Vectors(v.0.22.0), scales(v.1.0.0), ngsReports(v.1.1.1), BiocGenerics(v.0.30.0), pander(v.0.6.3), magrittr(v.1.5), forcats(v.0.4.0), stringr(v.1.4.0), dplyr(v.0.8.3), purrr(v.0.3.2), readr(v.1.3.1), tidyr(v.0.8.3), tibble(v.2.1.3), ggplot2(v.3.2.1), tidyverse(v.1.2.1), edgeR(v.3.26.8) and limma(v.3.40.6)

loaded via a namespace (and not attached): colorspace(v.1.4-1), hwriter(v.1.3.2), XVector(v.0.24.0), ggdendro(v.0.1-20), rstudioapi(v.0.10), lubridate(v.1.7.4), xml2(v.1.2.2), leaps(v.3.0), knitr(v.1.24), zeallot(v.0.1.0), jsonlite(v.1.6), Rsamtools(v.2.0.0), Cairo(v.1.5-10), broom(v.0.5.2), cluster(v.2.1.0), shiny(v.1.3.2), compiler(v.3.6.1), httr(v.1.4.1), backports(v.1.1.4), assertthat(v.0.2.1), Matrix(v.1.2-17), lazyeval(v.0.2.2), cli(v.1.1.0), later(v.0.8.0), htmltools(v.0.3.6), tools(v.3.6.1), gtable(v.0.3.0), glue(v.1.3.1), GenomeInfoDbData(v.1.2.1), reshape2(v.1.4.3), FactoMineR(v.1.42), ShortRead(v.1.42.0), fastmatch(v.1.1-0), Biobase(v.2.44.0), cellranger(v.1.1.0), vctrs(v.0.2.0), Biostrings(v.2.52.0), nlme(v.3.1-141), crosstalk(v.1.0.0), xfun(v.0.9), rvest(v.0.3.4), mime(v.0.7), XML(v.3.98-1.20), zlibbioc(v.1.30.0), MASS(v.7.3-51.4), zoo(v.1.8-6), promises(v.1.0.1), hms(v.0.5.1), SummarizedExperiment(v.1.14.1), rhdf5(v.2.28.0), RColorBrewer(v.1.1-2), yaml(v.2.2.0), gridExtra(v.2.3), latticeExtra(v.0.6-28), stringi(v.1.4.3), highr(v.0.8), BiocParallel(v.1.18.1), truncnorm(v.1.0-8), rlang(v.0.4.0), pkgconfig(v.2.0.2), bitops(v.1.0-6), matrixStats(v.0.55.0), evaluate(v.0.14), lattice(v.0.20-38), Rhdf5lib(v.1.6.0), GenomicAlignments(v.1.20.1), htmlwidgets(v.1.3), labeling(v.0.3), tidyselect(v.0.2.5), plyr(v.1.8.4), R6(v.2.4.0), generics(v.0.0.2), DelayedArray(v.0.10.0), pillar(v.1.4.2), haven(v.2.1.1), withr(v.2.1.2), scatterplot3d(v.0.3-41), RCurl(v.1.95-4.12), modelr(v.0.1.5), crayon(v.1.3.4), plotly(v.4.9.0), rmarkdown(v.1.15), locfit(v.1.5-9.1), readxl(v.1.3.1), data.table(v.1.12.2), digest(v.0.6.20), flashClust(v.1.01-2), webshot(v.0.5.1), xtable(v.1.8-4), httpuv(v.1.5.1), munsell(v.0.5.0), viridisLite(v.0.3.0) and kableExtra(v.1.1.0)